Ribonuclease P structure and function inArchaea

An important approach to understanding RNA-based catalytic function by ribonuclease P is the investigation of its evolutionary diversity in structure and function. Because RNase P enzymes from all organisms are thought to share common ancestry, the fundamental features of structure and biochemistry should be conserved in all of its modern forms. In contrast to the bacterial enzyme, the RNase P enzymes fromEucarya, organelles, andArchaea are poorly understood. This review describes our nascent understanding of the structure and function of RNase P inArchaea, and how this enzyme compares to its homologs in the other evolutionary Domains.Abbreviations RNase P ribonuclease P - tRNA transfer RNA - pre-tRNA 5-unprocessed precursor transfer RNA - Archaea a.k.a. archaebacteria - Bacteria a.k.a. eubacteria - Eucarya a.k.a. eukaryotic nucleus/cytoplasm     

Phylogeny of Dissimilatory Sulfite Reductases Supports an Early Origin of Sulfate Respiration

Microorganisms that use sulfate as a terminal electron acceptor for anaerobic respiration play a central role in the global sulfur cycle. Here, we report the results of comparative sequence analysis of dissimilatory sulfite reductase (DSR) genes from closely and distantly related sulfate-reducing organisms to infer the evolutionary history of DSR. A 1.9-kb DNA region encoding most of the α and β subunits of DSR could be recovered only from organisms capable of dissimilatory sulfate reduction with a PCR primer set targeting highly conserved regions in these genes. All DNA sequences obtained were highly similar to one another (49 to 89% identity), and their inferred evolutionary relationships were nearly identical to those inferred on the basis of 16S rRNA. We conclude that the high similarity of bacterial and archaeal DSRs reflects their common origin from a conserved DSR. This ancestral DSR was either present before the split between the domains Bacteria, Archaea, and Eucarya or laterally transferred between Bacteria and Archaea soon after domain divergence. Thus, if the physiological role of the DSR was constant over time, then early ancestors of Bacteria and Archaea already possessed a key enzyme of sulfate and sulfite respiration.     

微生物对低温极端环境适应性的研究进展

嗜冷微生物是地球寒冷环境中最主要的生物类群,并且是驱动全球生物地球化学循环的关键环节。嗜冷微生物在适应策略上显示出应对多种极端环境因素的巨大潜力,研究其适应和进化机制有助于更好地理解微生物与环境之间相互作用过程,并有效利用极端环境微生物资源。近年来,随着分子生物学和基因组学技术的高速发展,对微生物适应寒冷环境的机制及嗜冷微生物在指示气候变化和工农业应用方面均有一系列的突破。在此,本文将从基因组的GC含量、蛋白质稳定性、转录翻译调控、细胞膜流动性、渗透压调节、抗氧化损失和基因组适应性进化等方面总结当前在微生物适应低温环境机制上所取得的进展,并展望低温环境微生物在指示气候变化和工农业应用中的前景。     

Microbial Diversity in Caves

Relatively stable physical conditions in caves allow for the examination of the relationship between geochemical processes and the activity of microorganisms, reflected in substantial rock alterations, formation of new structures, surface deterioration and cave expansion. Although caves are considered as extreme environments, they are inhabited by microbial communities with unexpected diversity. While Proteobacteria and Actinobacteria are the most ubiquitous groups, also the presence of Archaea has been frequently noted recently. Here, we present a summary of results on diversity of cave microorganisms in the context of taxon distribution as well as the contribution and role of individual taxa in cave ecosystems.     

Fungal septins: one ring to rule it all?

Septins are a conserved family of GTP-binding proteins found in living organisms ranging from yeasts to mammals. They are able to polymerize and form hetero-oligomers that assemble into higher-order structures whose detailed molecular architecture has recently been described in different organisms. In Saccharomyces cerevisiae, septins exert numerous functions throughout the cell cycle, serving as scaffolds for many different proteins or as diffusion barriers at the bud neck. In other fungi, septins are required for the proper completion of diverse functions such as polarized growth or pathogenesis. Recent results from several fungi have revealed important differences in septin organization and regulation as compared with S. cerevisiae, especially during Candida albicans hyphal growth and in Ashbya gossypii. Here we focus on these recent findings, their relevance in the biology of these eukaryotes and in consequence the “renaissance” of the study of septin structures in cells showing a different kind of morphological behaviour.     

Sex, Death, and Evolution in Proto- and Metazoa, 1876–1913

In the period 1875–1920, a debate about the generality and applicability of evolutionary theory to all organisms was motivated by work on unicellular ciliates like Paramecium because of their peculiar nuclear dualism and life cycles. The French cytologist Emile Maupas and the German zoologist August Weismann argued in the 1880s about the evolutionary origins and functions of sex (which in the ciliates is not linked to reproduction), and death (which appeared to be the inevitable fate of lineages denied sexual conjugation), an argument rooted in the question of whether the ciliates and their processes where homologous to other cellular organisms. In the beginning of the twentieth century, this question of homology came to be less important as the ciliates were used by the British protozoologist Clifford Dobell and the American zoologist Herbert Spencer Jennings to study evolutionary processes in general rather than problems of development and cytology. For them, homology mattered less than analogy. This story illustrates two partially distinct problems in evolutionary biology: first, the question of whether all living things have common features and origins; and second, whether their history and current nature can be described by identical mechanisms. Where Maupas (contra Weismann) made the ciliates qualitatively the same as all other organisms in order to create a cohesive evolutionary theory for biology, Jennings and Dobell made them qualitatively different in order to achieve the same end. This revised version was published online in July 2006 with corrections to the Cover Date.     

Evolutionary Transitions Among Dinosaurs: Examples from the Jurassic of China

Dinosaurs have captured the popular imagination more than any other extinct group of organisms and are therefore a powerful tool in teaching evolutionary biology. Most students are familiar with a wide variety of dinosaurs and the relative suddenness of their extinction, but few are aware of the tremendous longevity of their time on Earth and the richness of their fossil record. We first review some of the best-known groups of dinosaurs and discuss how their less-specialized relatives elucidate the path through which each evolved. We then discuss our recent discovery of Yinlong downsi, a distant relative of Triceratops, and other fossils from Jurassic deposits in China to exemplify how the continuing discovery of fossils is filling out the dinosaur family tree.     

Speciation in protists: Spatial and ecological divergence processes cause rapid species diversification in a freshwater chrysophyte

Although eukaryotic microorganisms are extremely numerous, diverse and essential to global ecosystem functioning, they are largely understudied by evolutionary biologists compared to multicellular macroscopic organisms. In particular, very little is known about the speciation mechanisms which may give rise to the diversity of microscopic eukaryotes. It was postulated that the enormous population sizes and ubiquitous distribution of these organisms could lead to a lack of population differentiation and therefore very low speciation rates. However, such assumptions have traditionally been based on morphospecies, which may not accurately reflect the true diversity, missing cryptic taxa. In this study, we aim to articulate the major diversification mechanisms leading to the contemporary molecular diversity by using a colonial freshwater flagellate, Synura sphagnicola, as an example. Phylogenetic analysis of five sequenced loci showed that S. sphagnicola differentiated into two morphologically distinct lineages approximately 15.4 million years ago, which further diverged into several evolutionarily recent haplotypes during the late Pleistocene. The most recent haplotypes are ecologically and biogeographically much more differentiated than the old lineages, presumably because of their persistent differentiation after the allopatric speciation events. Our study shows that in microbial eukaryotes, species diversification via the colonization of new geographical regions or ecological resources occurs much more readily than was previously thought. Consequently, divergence times of microorganisms in some lineages may be equivalent to the estimated times of speciation in plants and animals.     

Microbial Ecology of an Extreme Acidic Environment, the Tinto River

The Tinto River (Huelva, southwestern Spain) is an extreme environment with a rather constant acidic pH along the entire river and a high concentration of heavy metals. The extreme conditions of the Tinto ecosystem are generated by the metabolic activity of chemolithotrophic microorganisms thriving in the rich complex sulfides of the Iberian Pyrite Belt. Molecular ecology techniques were used to analyze the diversity of this microbial community. The community's composition was studied by denaturing gradient gel electrophoresis (DGGE) using 16S rRNA and by 16S rRNA gene amplification. A good correlation between the two approaches was found. Comparative sequence analysis of DGGE bands showed the presence of organisms related to Leptospirillum spp., Acidithiobacillus ferrooxidans, Acidiphilium spp., “Ferrimicrobium acidiphilum,” Ferroplasma acidiphilum, and Thermoplasma acidophilum. The different phylogenetic groups were quantified by fluorescent in situ hybridization with a set of rRNA-targeted oligonucleotide probes. More than 80% of the cells were affiliated with the domain Bacteria, with only a minor fraction corresponding to Archaea. Members of Leptospirillum ferrooxidans, Acidithiobacillus ferrooxidans, and Acidiphilium spp., all related to the iron cycle, accounted for most of the prokaryotic microorganisms detected. Different isolates of these microorganisms were obtained from the Tinto ecosystem, and their physiological properties were determined. Given the physicochemical characteristics of the habitat and the physiological properties and relative concentrations of the different prokaryotes found in the river, a model for the Tinto ecosystem based on the iron cycle is suggested.     

The evolutionary ecology of Plasmodium

Plasmodium, the aetiological agent of malaria, imposes a substantial public health burden on human society and one that is likely to deteriorate. Hitherto, the recent Darwinian medicine movement has promoted the important role evolutionary biology can play in issues of public health. Recasting the malaria parasite two‐host life cycle within an evolutionary framework has generated considerable insight into how the parasite has adapted to life within both vertebrate and insect hosts. Coupled with the rapid advances in the molecular basis to host–parasite interactions, exploration of the evolutionary ecology of Plasmodium will enable identification of key steps in the life cycle and highlight fruitful avenues of research for developing malaria control strategies. In addition, elucidating the extent to which Plasmodium can respond to short‐ and long‐term changes in selection pressures, i.e. its adaptive capacity, is even more crucial in predicting how the burden of malaria will alter with our rapidly evolving ecology.     

Molecular analysis of methanogenic archaeal communities in managed and natural upland pasture soils

Grassland management influences soil archaeal communities, which appear to be dominated by nonthermophilic crenarchaeotes. To determine whether methanogenic Archaea associated with the Euryarchaeota lineage are also present in grassland soils, anaerobic microcosms containing both managed (improved) and natural (unimproved) grassland rhizosphere soils were incubated for 28 days to encourage the growth of anaerobic Archaea. The contribution of potential methanogenic organisms to the archaeal community was assessed by the molecular analysis of RNA extracted from soil, using primers targeting all Archaea and Euryarchaeota. Archaeal RT‐PCR products were obtained from all anaerobic microcosms. However, euryarchaeal RT‐PCR products (of putative methanogen origin) were obtained only from anaerobic microcosms of improved soil, their presence coinciding with detectable methane production. Sequence analysis of excised denaturing gradient gel electrophoresis (DGGE) bands revealed the presence of euryarchaeal organisms that could not be detected before anaerobic enrichment. These data indicate that nonmethanogenic Crenarchaeota dominate archaeal communities in grassland soil and suggest that management practices encourage euryarchaeal methanogenic activity.     

A novel regulation on developmental gene expression of fruiting body formation in Myxobacteria

Myxobacteria are Gram-negative soil microorganisms that prey on other microorganisms. Myxobacteria have significant potential for applications in biotechnology because of their extraordinary ability to produce natural products such as secondary metabolites. Myxobacteria also stand out as model organisms for the study of cell–cell interactions and multicellular development during their complex life cycle. Cellular morphogenesis during multicellular development in myxobacteria is very similar to that in the eukaryotic soil amoebae. Recent studies have started uncovering molecular mechanisms directing the myxobacterial life cycle. We describe recent studies on signal transduction and gene expression during multicellular development in the myxobacterium Myxococcus xanthus. We provide our current model for signal transduction pathways mediated by a two-component His–Asp phosphorelay system and a Ser/Thr kinase cascade.     

Molecular Characterization of an Endolithic Microbial Community in Dolomite Rock in the Central Alps (Switzerland)

Endolithic microorganisms colonize the pores in exposed dolomite rocks in the Piora Valley in the Swiss Alps. They appear as distinct grayish-green bands about 1–8 mm below the rock surface. Based on environmental small subunit ribosomal RNA gene sequences, a diverse community driven by photosynthesis has been found. Cyanobacteria (57 clones), especially the genus Leptolyngbya, form the functional basis for an endolithic community which contains a wide spectrum of so far not characterized species of chemotrophic Bacteria (64 clones) with mainly Actinobacteria, Alpha-Proteobacteria, Bacteroidetes, and Acidobacteria, as well as a cluster within the Chloroflexaceae. Furthermore, a cluster within the Crenarchaeotes (40 clones) has been detected. Although the eukaryotic diversity was outside the scope of the study, an amoeba (39 clones), and several green algae (51 clones) have been observed. We conclude that the bacterial diversity in this endolithic habitat, especially of chemotrophic, nonpigmented organisms, is considerable and that Archaea are present as well.     

Serpins in Unicellular Eukarya, Archaea, and Bacteria: Sequence Analysis and Evolution

Most serpins irreversibly inactivate specific serine proteinases of the chymotrypsin family. Inhibitory serpins are unusual proteins in that their native structure is metastable, and rapid conversion to a relaxed state is required to trap target enzymes in a covalent complex. The evolutionary origin of the serpin fold is unresolved, and while serpins in animals are known to be involved in the regulation of a remarkable diversity of metabolic processes, the physiological functions of homologues from other phyla are unknown. Addressing these questions, here we analyze serpin genes identified in unicellular eukaryotes: the green alga Chlamydomonas reinhardtii, the dinoflagellate Alexandrium tamarense, and the human pathogens Entamoeba spp., Eimera tenella, Toxoplasma gondii, and Giardia lamblia. We compare these sequences to others, particularly those in the complete genome sequences of Archaea, where serpins were found in only 4 of 13 genera, and Bacteria, in only 9 of 56 genera. The serpins from unicellular organisms appear to be phylogenetically distinct from all of the clades of higher eukaryotic serpins. Most of the sequences from unicellular organisms have the characteristics of inhibitory serpins, and where multiple serpin genes are found in one genome, variability is displayed in the region of the reactive-center loop important for specificity. All the unicellular eukaryotic serpins have large hydrophobic or positively charged residues at the putative P₁ position. In contrast, none of the prokaryotic serpins has a residue of these types at the predicted P₁ position, but many have smaller, neutral residues. Serpin evolution is discussed.[Reviewing Editor: Dr. Peer Bork]     

Myxomycete diversity and distribution from the fossil record to the present

The myxomycetes (plasmodial slime molds or myxogastrids) are a group of eukaryotic microorganisms usually present and sometimes abundant in terrestrial ecosystems. Evidence from molecular studies suggests that the myxomycetes have a significant evolutionary history. However, due to the fragile nature of the fruiting body, fossil records of the group are exceedingly rare. Although most myxomycetes are thought to have very large distributional ranges and many species appear to be cosmopolitan or nearly so, results from recent studies have provided evidence that spatial distribution patterns of these organisms can be successfully related to (1) differences in climate and/or vegetation on a global scale and (2) the ecological differences that exist for particular habitats on a local scale. A detailed examination of the global distribution of four examples (Barbeyella minutissima, Ceratiomyxa morchella, Leocarpus fragilis and Protophysarum phloiogenum) demonstrates that these species have recognizable distribution patterns in spite of the theoretical ability of their spores to bridge continents. Special Issue: Protist diversity and geographic distribution. Guest editor: W. Foissner.     

Presidential address: rediscovering parasites using molecular tools--towards revising the taxonomy of Echinococcus, Giardia and Cryptosporidium

Molecular biology has provided parasitologists with a fantastic variety of techniques that have had a major impact on research into parasites and parasitism. Molecular tools have revealed the extent and nature of genetic diversity in parasites and this information has made a significant contribution to studies on the population genetics and evolutionary biology of parasites. Similarly, epidemiology has benefited enormously from the application of molecular tools in terms of studying parasite life cycles and transmission, and in the development of specific and sensitive methods for diagnosis and surveillance. However, the theme I wish to develop in this paper is concerned with the contribution molecular tools have made to parasite taxonomy and systematics, and in particular, the fact that in many cases molecular tools are validating the proposals made many years ago by taxonomists and biologists which were discounted or not fully accepted at the time. To do this I have chosen four examples (Echinococcus, Entamoeba, Giardia, Cryptosporidium) where recent research involving molecular characterisation has confirmed observations made many years ago and has resulted in a need to revise the taxonomy of different groups of parasites.     

Organic Codes: A Unifying Concept for Life

Although the knowledge about biological systems has advanced exponentially in recent decades, it is surprising to realize that the very definition of Life keeps presenting theoretical challenges. Even if several lines of reasoning seek to identify the essence of life phenomenon, most of these thoughts contain fundamental problem in their basic conceptual structure. Most concepts fail to identify either necessary or sufficient features to define life. Here, we analyzed the main conceptual frameworks regarding theoretical aspects that have been supporting the most accepted concepts of life, such as (i) the physical, (ii) the cellular and (iii) the molecular approaches. Based on an ontological analysis, we propose that Life should not be positioned under the ontological category of Matter. Yet, life should be better understood under the top-level ontology of “Process”. Exercising an epistemological approach, we propose that the essential characteristic that pervades each and every living being is the presence of organic codes. Therefore, we explore theories in biosemiotics and code biology in order to propose a clear concept of life as a macrocode composed by multiple inter-related coding layers. This way, as life is a sort of metaphysical process of encoding, the living beings became the molecular materialization of that process. From the proposed concept, we show that the evolutionary process is a fundamental characteristic for life’s maintenance but it is not necessary to define life, as many organisms are clearly alive but they do not participate in the evolutionary process (such as infertile hybrids). The current proposition opens a fertile field of debate in astrobiology, epistemology, biosemiotics, code biology and robotics.

     

Rationalizing Early Embryogenesis in the 1930s: Albert Dalcq on Gradients and Fields

The present account aims to contribute to a better characterization of the state and the dynamics of embryological knowledge at the dawn of the molecular revolution in biology. In this study, Albert Dalcq (1893–1973) was chosen as a representative of a generation of embryologists who found themselves at the junction of two very different approaches to the study of life: the first, focusing on global properties of organisms; the second focusing on the characterization of basic molecular constituents. Though clearly belonging to the organismic tradition, Dalcq was already blending his experimental and explanatory practices with biochemical aspects by the 1930s. Principally based on published sources, the present analysis focuses on the conceptual definitions, modifications and interrelations on which Dalcq's explanation of development rested. Among these are variant process concepts such as gradients and fields, which are often thought to have strongly holistic implications. I will argue that Dalcq's version of these concepts was compatible with a more reductionist treatment of embryos than was accepted by most embryologists as late as the 1950s, pointing to some extent toward the recent molecular characterization of gradients by molecular geneticists such as Christiane Nüsslein-Volhard. Moreover, I will show how the embryological research program of Dalcq and his pupil Jean Brachet has been largely instrumental in the development of molecular biology in Belgium. This revised version was published online in July 2006 with corrections to the Cover Date.     

Selective enrichment,isolation and molecular detection of <Emphasis Type="Italic">Salinibacter</Emphasis> and related extremely halophilic <Emphasis Type="Italic">Bacteria</Emphasis> from hypersaline environments

Salinibacter is a genus of red, extremely halophilic Bacteria. Thus far the genus is represented by a single species, Salinibacter ruber, strains of which have been isolated from saltern crystallizer ponds in Spain and on the Balearic Islands. Both with respect to its growth conditions and its physiology, Salinibacter resembles the halophilic Archaea of the order Halobacteriales. We have designed selective enrichment and isolation techniques to obtain Salinibacter and related red extremely halophilic Bacteria from different hypersaline environments, based on their resistance to anisomycin and bacitracin, two antibiotics that are potent inhibitors of the halophilic Archaea. Using direct plating on media containing bacitracin, we found Salinibacter-like organisms in numbers between 1.4×10³ and 1.4×10⁶ml⁻¹ in brines collected from the crystallizer ponds of the salterns in Eilat, Israel, being equivalent to 1.8–18% of the total colony counts obtained on identical media without bacitracin. A number of strains from Eilat were subjected to a preliminary characterization, and they proved similar to the type strain of S. ruber. We also report here the isolation and molecular detection of Salinibacter-like organisms from an evaporite crust on the bottom of salt pools at the Badwater site in Death Valley, CA. These isolates and environmental 16S rRNA gene sequences differ in a number of properties from S. ruber, and they may represent a new species of Salinibacter or a new related genus. Guest Editor: John M. Melack Saline Waters and their Biota     

Organisms of deep sea hydrothermal vents as a source for studying adaptation and evolution

It has been postulated that life originated in a similar environment to those of deep sea hydrothermal vents. These environments are located along volcanic ridges and are characterized by extreme conditions such as unique physical properties (temperature, pressure), chemical toxicity, and absence of photosynthesis. However, numerous living organisms have been discovered in these hostile environments, including a variety of microorganisms and many animal species which live in intimate and complex symbioses with sulfo-oxidizing and methanotrophic bacteria. Recent proteomic analyses of the endosymbiont ofRiftia pachyptila and genome sequences of some free living and symbiotic bacteria have provided complementary information about the potential metabolic and genomic capacities of these organisms. The evolution of these adaptive strategies is connected with different mechanisms of genetic adaptation including horizontal gene transfer and . various structural and functional mutations. Therefore, the organisms in this environment are good models for studying the evolution of prokaryotes and eukaryotes as well as different aspects of the biology of adaptation. This review describes some current research concerning metabolic and plausible genetic adaptations of organisms in a deep sea environment, usingRiftia pachyptila as model.